"""Module that contains functions for editing case-attribute data"""
from pathlib import Path
from typing import Optional
from dataclasses import dataclass
from enum import Enum, auto
import json
import pickle
import lmdb
class EditStatus(Enum):
"""Enumeration for the status of the edits."""
review = auto() # pylint: disable=[invalid-name]
approved = auto() # pylint: disable=[invalid-name]
rejected = auto() # pylint: disable=[invalid-name]
def __str__(self):
"""Print out human-readable form."""
return self.name
@dataclass
class CaseAttributeEdit:
"""Represents an edit operation for case attributes in the database.
Attributes:
- inbredset_id (int): The ID of the inbred set associated with
the edit.
- status: (EditStatus): The status of this edit.
- user_id (str): The ID of the user performing the edit.
- changes (dict): A dictionary containing the changes to be
applied to the case attributes.
"""
inbredset_id: int
status: EditStatus
user_id: str
changes: dict
def queue_edit(cursor, directory: Path, edit: CaseAttributeEdit) -> Optional[int]:
"""Queues a case attribute edit for review by inserting it into
the audit table and storing its review ID in an LMDB database.
Args:
cursor: A database cursor for executing SQL queries.
directory (Path): The base directory path for the LMDB database.
edit (CaseAttributeEdit): A dataclass containing the edit details, including
inbredset_id, status, user_id, and changes.
Returns:
int: An id the particular case-attribute that was updated.
"""
cursor.execute(
"INSERT INTO "
"caseattributes_audit(status, editor, json_diff_data) "
"VALUES (%s, %s, %s) "
"ON DUPLICATE KEY UPDATE status=%s",
(str(edit.status), edit.user_id,
json.dumps(edit.changes), str(EditStatus.review),))
directory.mkdir(parents=True, exist_ok=True)
env = lmdb.open(directory.as_posix(), map_size=8_000_000) # 1 MB
with env.begin(write=True) as txn:
review_ids = set()
if reviews := txn.get(b"review"):
review_ids = pickle.loads(reviews)
_id = cursor.lastrowid
review_ids.add(_id)
txn.put(b"review", pickle.dumps(review_ids))
return _id
def __fetch_case_attrs_changes__(cursor, change_ids: tuple) -> list:
"""Fetches case attribute change records from the audit table for
given change IDs.
Retrieves records from the `caseattributes_audit` table for the
specified `change_ids`, including the editor, JSON diff data, and
timestamp. The JSON diff data is deserialized into a Python
dictionary for each record. Results are ordered by timestamp in
descending order (most recent first).
Args:
cursor: A MySQLdb cursor for executing SQL queries.
change_ids (tuple): A tuple of integers representing the IDs
of changes to fetch.
Returns:
list: A list of dictionaries, each containing the `editor`,
`json_diff_data` (as a deserialized dictionary), and `time_stamp`
for the matching change IDs. Returns an empty list if no records
are found.
Notes:
- The function assumes `change_ids` is a non-empty tuple of valid integers.
- The `json_diff_data` column in `caseattributes_audit` is expected to contain valid
JSON strings, which are deserialized into dictionaries.
- The query uses parameterized placeholders to prevent SQL injection.
- This is an internal helper function (indicated by double underscores) used by
other functions like `get_changes`.
Raises:
json.JSONDecodeError: If any `json_diff_data` value cannot be deserialized.
TypeError: If `change_ids` is empty or contains non-integer values, potentially
causing a database error.
"""
if not change_ids:
return {} # type:ignore
placeholders = ','.join(['%s'] * len(change_ids))
cursor.execute(
"SELECT editor, json_diff_data, time_stamp "
f"FROM caseattributes_audit WHERE id IN ({placeholders}) "
"ORDER BY time_stamp DESC",
change_ids
)
results = cursor.fetchall()
for el in results:
el["json_diff_data"] = json.loads(el["json_diff_data"])
return results
def view_change(cursor, change_id: int) -> dict:
"""Queries the `caseattributes_audit` table to fetch the
`json_diff_data` column for the given `change_id`. The JSON data
is deserialized into a Python dictionary and returned. If no
record is found or the `json_diff_data` is None, an empty
dictionary is returned.
Args:
cursor: A MySQLdb cursor for executing SQL queries.
change_id (int): The ID of the change to retrieve from the
`caseattributes_audit` table.
Returns:
dict: The deserialized JSON diff data as a dictionary if the
record exists and contains valid JSON; otherwise, an
empty dictionary.
Raises:
json.JSONDecodeError: If the `json_diff_data` cannot be
deserialized due to invalid JSON.
TypeError: If `cursor.fetchone()` returns None (e.g., no
record found) and `json_diff_data` is accessed, though the
function handles this by returning an empty dictionary.
"""
cursor.execute(
"SELECT json_diff_data "
"FROM caseattributes_audit "
"WHERE id = %s",
(change_id,)
)
json_diff_data, _ = cursor.fetchone()
if json_diff_data:
json_diff_data = json.loads(json_diff_data)
return json_diff_data
return {}
def get_changes(cursor, change_type: EditStatus, directory: Path) -> dict:
"""Retrieves case attribute changes for given lmdb data in
directory categorized by review status.
Fetches change IDs from an LMDB database, categorized into the
"data" key based on the EditStatus
Args:
- cursor: A MySQLdb cursor for executing SQL queries.
- change_type (EditStatus): The status of changes to retrieve
('review', 'approved', or 'rejected').
- directory (Path): The base directory path for the LMDB
database.
Returns:
dict: A dictionary with two keys:
-'count': A dictionary with counts of 'reviews',
'approvals' and 'rejections'.
- 'data': contains the json diff data of the modified data
Raises:
json.JSONDecodeError: If any `json_diff_data` in the audit
table cannot be deserialized by
`__fetch_case_attrs_changes__`.
TypeError: If `inbredset_id` is not an integer or if LMDB data
cannot be deserialized. Also raised when an invalid change_id
is used.
"""
directory.mkdir(parents=True, exist_ok=True)
review_ids, approved_ids, rejected_ids = set(), set(), set()
directory.mkdir(parents=True, exist_ok=True)
env = lmdb.open(directory.as_posix(), map_size=8_000_000) # 1 MB
with env.begin(write=False) as txn:
if reviews := txn.get(b"review"):
review_ids = pickle.loads(reviews)
if approvals := txn.get(b"approved"):
approved_ids = pickle.loads(approvals)
if rejections := txn.get(b"rejected"):
rejected_ids = pickle.loads(rejections)
changes = {}
match change_type:
case EditStatus.review:
changes = dict(
zip(review_ids,
__fetch_case_attrs_changes__(cursor, tuple(review_ids)))
)
case EditStatus.approved:
changes = dict(
zip(approved_ids,
__fetch_case_attrs_changes__(cursor, tuple(approved_ids)))
)
case EditStatus.rejected:
changes = dict(zip(rejected_ids,
__fetch_case_attrs_changes__(cursor, tuple(rejected_ids))))
case _:
raise TypeError
return {
"change-type": str(change_type),
"count": {
"reviews": len(review_ids),
"approvals": len(approved_ids),
"rejections": len(rejected_ids)
},
"data": changes
}
# pylint: disable=[too-many-locals, too-many-branches]
def apply_change(cursor, change_type: EditStatus, change_id: int, directory: Path) -> bool:
"""Applies or rejects a case attribute change and updates its
status in the audit table and LMDB.
Processes a change identified by `change_id` based on the
specified `change_type` (approved or rejected). For approved
changes, applies modifications to the `CaseAttributeXRefNew` table
using bulk inserts and updates the audit status. For rejected
changes, updates the audit status only. Manages change IDs in
LMDB by moving them from the 'review' set to either 'approved' or
'rejected' sets. Returns False if the `change_id` is not in the
review set.
Args:
cursor: A MySQLdb cursor for executing SQL queries.
change_type (EditStatus): The action to perform, either
`EditStatus.approved` or `EditStatus.rejected`.
change_id (int): The ID of the change to process,
corresponding to a record in `caseattributes_audit`.
directory (Path): The base directory path for the LMDB
database.
Returns:
bool: True if the change was successfully applied or rejected,
False if `change_id` is not found in the LMDB 'review'
set.
Notes:
- Opens an LMDB environment in the specified `directory` with
a map size of 8 MB.
- For `EditStatus.approved`, fetches `json_diff_data` from
`caseattributes_audit`, extracts modifications, and performs
bulk inserts into `CaseAttributeXRefNew` with `ON DUPLICATE
KEY UPDATE`.
- For `EditStatus.rejected`, updates the
`caseattributes_audit` status without modifying case
attributes.
- Uses bulk `SELECT` queries to fetch `StrainId` and
`CaseAttributeId` values efficiently.
- Assumes `CaseAttributeXRefNew` has a unique key on
`(InbredSetId, StrainId, CaseAttributeId)` for `ON DUPLICATE
KEY UPDATE`.
- The `json_diff_data` is expected to contain valid JSON with
an `inbredset_id` and `Modifications.Current` structure.
- The second column from `fetchone()` is ignored (denoted by
`_`).
Raises:
ValueError: If `change_type` is neither `EditStatus.approved`
nor `EditStatus.rejected`.
json.JSONDecodeError: If `json_diff_data` cannot be
deserialized for approved changes.
TypeError: If `cursor.fetchone()` returns None for
`json_diff_data` or if `strain_id` or `caseattr_id` are
missing during bulk insert preparation.
pickle.UnpicklingError: If LMDB data (e.g., 'review' or
'approved' sets) cannot be deserialized.
"""
review_ids, approved_ids, rejected_ids = set(), set(), set()
directory.mkdir(parents=True, exist_ok=True)
env = lmdb.open(directory.as_posix(), map_size=8_000_000) # 1 MB
with env.begin(write=True) as txn:
if reviews := txn.get(b"review"):
review_ids = pickle.loads(reviews)
if change_id not in review_ids:
return False
match change_type:
case EditStatus.rejected:
cursor.execute(
"UPDATE caseattributes_audit "
"SET status = %s "
"WHERE id = %s",
(str(change_type), change_id))
if rejections := txn.get(b"rejected"):
rejected_ids = pickle.loads(rejections)
rejected_ids.add(change_id)
review_ids.discard(change_id)
txn.put(b"review", pickle.dumps(review_ids))
txn.put(b"rejected", pickle.dumps(rejected_ids))
return True
case EditStatus.approved:
cursor.execute(
"SELECT json_diff_data "
"FROM caseattributes_audit WHERE "
"id = %s",
(change_id,)
)
result = cursor.fetchone()
if result is None:
return False
json_diff_data = result[0]
json_diff_data = json.loads(json_diff_data)
inbredset_id = json_diff_data.get("inbredset_id")
modifications = json_diff_data.get(
"Modifications", {}).get("Current", {})
strains = tuple(modifications.keys())
case_attrs = set()
for data in modifications.values():
case_attrs.update(data.keys())
# Bulk fetch strain ids
strain_id_map = {}
if strains:
cursor.execute(
"SELECT Name, Id FROM Strain WHERE Name IN "
f"({', '.join(['%s'] * len(strains))})",
strains
)
for name, strain_id in cursor.fetchall():
strain_id_map[name] = strain_id
# Bulk fetch case attr ids
caseattr_id_map = {}
if case_attrs:
cursor.execute(
"SELECT Name, CaseAttributeId FROM CaseAttribute "
"WHERE InbredSetId = %s AND Name IN "
f"({', '.join(['%s'] * len(case_attrs))})",
(inbredset_id, *case_attrs)
)
for name, caseattr_id in cursor.fetchall():
caseattr_id_map[name] = caseattr_id
# Bulk insert data
insert_data = []
for strain, data in modifications.items():
strain_id = strain_id_map.get(strain)
for case_attr, value in data.items():
insert_data.append({
"inbredset_id": inbredset_id,
"strain_id": strain_id,
"caseattr_id": caseattr_id_map.get(case_attr),
"value": value,
})
if insert_data:
cursor.executemany(
"INSERT INTO CaseAttributeXRefNew "
"(InbredSetId, StrainId, CaseAttributeId, Value) "
"VALUES (%(inbredset_id)s, %(strain_id)s, %(caseattr_id)s, %(value)s) "
"ON DUPLICATE KEY UPDATE Value = VALUES(Value)",
insert_data
)
# Update LMDB and audit table
cursor.execute(
"UPDATE caseattributes_audit "
"SET status = %s "
"WHERE id = %s",
(str(change_type), change_id))
if approvals := txn.get(b"approved"):
approved_ids = pickle.loads(approvals)
approved_ids.add(change_id)
review_ids.discard(change_id)
txn.put(b"review", pickle.dumps(review_ids))
txn.put(b"approved", pickle.dumps(approved_ids))
return True
case _:
raise ValueError
